7BXV

11A1 antibody-peptide complex

• PDB DOI: https://doi.org/10.2210/pdb7BXV/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Mutation(s): No 


• Deposited: 2020-04-21 Released: 2021-04-21 
• Deposition Author(s): Irie, K., Irie, Y., Kita, A., Miki, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.194 
• R-Value Work: 0.166 

Literature

APOE epsilon 4 allele advances the age-dependent decline of amyloid beta clearance in the human cortex.

Saito, A., Kageyama, Y., Pletnikova, O., Rudow, G.L., An, Y., Irie, Y., Kita, A., Miki, K., Li, L., Southall, P., Irie, K., Troncoso, J.C.

(2022) Biorxiv 

• DOI: https://doi.org/10.1101/2021.04.07.438832

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 48.64 kDa 
• Atom Count: 3,816 
• Modelled Residue Count: 439 
• Deposited Residue Count: 440 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab of the 11A1 antibody L chain	A [auth L]	217	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab of the 11A1 antibody H chain	B [auth H]	218	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TYR-GLU-VAL-HIS-HIS	C [auth A]	5	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO (Subject of Investigation/LOI)	D [auth L], E [auth L], F [auth H], G [auth H], H	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.194 
• R-Value Work: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.639	α = 90
b = 123.774	β = 99.743
c = 45.692	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-04-21 
Deposition Author(s): Irie, K., Irie, Y., Kita, A., Miki, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19H00921

Revision History  

• Version 1.0: 2021-04-21
  Type: Initial release
  
• Version 1.1: 2022-05-04
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description